Automatic segmentation for enhanced quantification of fungi in transgenic mice

Esther Klaile, Jan-Philipp Praetorius, Marc Thilo Figge, Hortense Slevogt

Intestine-on-chip modeling and automated image analysis reveal a proinflammatory potential of sterile fecal microbiome filtrate from ulcerative colitis patients

Tobias Schaal, Parastoo Akbarimoghaddam, Valentin Wegner, Arndt Steube, Elena Gardey, Adrian Feile, Mohamed Abdelwahab Hassan, Zoltán Cseresnyés, Alexander Mosig, Andreas Stallmach, Marc Thilo Figge, Johannes Stallhofer

Journal of Crohn's and Colitis

Complex-mediated evasion: modeling defense against antimicrobial peptides with application to human-pathogenic fungus Candida albicans

Yann Bachelot, Anastasia Solomatina, Marc Thilo Figge

Rapid detection of microbial antibiotic susceptibility via deep learning supported analysis of angle-resolved scattered-light images of picoliter droplet cultivations

Martina Graf , Arjun Sarkar, Carl-Magnus Svensson, Anne-Sophie Munser, Sven Schroder , Sundar Hengoju, Miriam A. Rosenbaum, Marc Thilo Figge

Sensors and Actuators: B. Chemical

Spatiotemporal modeling quantifies cellular contribution to uptake of Aspergillus fumigatus in the human lung

Saffer C, Timme S, Ortiz CS, Bertuzzi M, Figge MT

Competitive Inhibition and Mutualistic Growth in Polymicrobial Infections: Deciphering Staphylococcus aureus – Acinetobacter baumannii Interaction Dynamics

Sandra Timme 1(*), Sindy Wendler 2(*), Tilman Klassert 3,4, Joao Pedro Saraiva5, Ulisses Nunes da Rocha5, Manuel Wittchen 6, Sareda Schramm 7, Ralf Ehricht 8, 9, Stefan Monecke 8, 10, Birgit Edel 2, Jürgen Rödel 2, Bettina Löffler 2, Maria Soledad Ramirez 7, Hortense Slevogt 3,4, Marc Thilo Figge 1,11 (*¥), Lorena Tuchscherr 2 (*¥)

Nature Communications

Nanobody-mediated neutralization of candidalysin prevents epithelial damage and inflammatory responses that drive vulvovaginal candidiasis pathogenesis

Marisa Valentine*, Paul Rudolph*, Axel Dietschmann, Antzela Tsavoud, Selene Mogavero, Sejeong Leed, Emily L. Priestd, Gaukhar Zhurgenbayeva,Nadja Jablonowskia, Sandra Timme, Christian Eggeling,Stefanie Allert, Edward Dolk, Julian R. Naglik, Marc T. Figge,Mark S. Gresnigt*#, Bernhard Hube*#

mBio

Deep learning-based characterization of neutrophil activation phenotypes in ex vivo human Candida blood infections

Arjun Sarkar, Jan-Philipp Praetorius, Marc Thilo Figge

Long-term stimulation by implanted pacemaker enables non-atrophic treatment of vocal fold paresis in a human-like animal model

Kassandra Walluks, Bianca Hoffmann, Carl-Magnus Svensson, Gerhard Förster, Andreas H. Müller, Jonathan Jarvis, Justin Perkins, Marc Thilo Figge, Dirk Arnold

Modeling of intravenous caspofungin administration using an intestine-on-chip reveals altered Candida albicans microcolonies and pathogenicity

Tim Kaden, Raquel Alonso-Román, Parastoo Akbarimoghaddam, Alexander S. Mosig, Katja Graf, Martin Raasch, Bianca Hoffmann, Marc T. Figge, Bernhard Hube, Mark S. Gresnigt

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division

Eric Ruhland [1, 2], Malte Siemers [1, 2, 4], Ruman Gerst [1, 3, 4], Felix Späth [1], Laura Vogt [1], Marc-Thilo Figge [1, 2, 3], Kai Papenfort [1, 2], Kathrin Sophie Fröhlich [1, 2, *]

PNAS

Long-term stimulation by implanted pacemaker enables non-atrophic treatment of vocal fold paresis in a human-like animal model

Kassandra Walluks, Bianca Hoffmann, Carl-Magnus Svensson, Gerhard Förster, Andreas H. Müller, Justin Perkins, Marc Thilo Figge, Dirk Arnold

Unique target binding by the C-terminal region of FHR1 provides a new perception for aHUS Pathology

Perie L, Stippa S, Saffer C, Hartmann A, Mörgelin M, Zipfel SLH, Figge MT, Wiech T, Skerka C, Zipfel PF

Blood

IMFSegNet: Cost-effective and objective quantification of intramuscular fat in histological sections by deep learning

Jan-Philipp Praetorius, Kassandra Walluks, Carl-Magnus Svensson, Dirk Arnold, Marc Thilo Figge

Quantitative Analysis of Peroxisome Tracks using a Hidden Markov Model

Svensson C-M, Reglinski K, Schliebs W, Erdmann R, Eggeling C, Figge MT

Scientific Reports

Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections

Saffer C, Timme S, Rudolph P, Figge MT

Nature Systems Biology and Application

JIPipe: A graphical batch processing language for ImageJ

Ruman Gerst, Zoltán Cseresnyés,Marc Thilo Figge

Toxin-producing endosymbionts shield pathogenic fungus against micropredators.

Richter, I., Radosa, S., Cseresnyés, Z., Ferling, I., Büttner, H., Niehs, S.P., Gerst, R., Figge, M.T., Hillmann, Falk, Hertweck, C.

mBio

Bacterial endosymbionts protect beneficial soil fungus from nematode attack

Büttner H*, Niehs SP*, Vandelannoote K, Cseresnyés Z, Dose B, Richter I, Gerst R, Figge MT, Stinear TP, Pidot SJ, Hertweck C

PNAS 118, 37.

Invasive aspergillosis-on-chip: A quantitative treatment study of human Aspergillus fumigatus infection.

Hoang, T. *, Cseresnyés, Z.*, Hartung, S.*, Blickensdorf, M., Saffer, C., Rennert, K., Mosig, A.S, von Lilienfeld-Toal, M.#+, Figge, M.T.#+

Biomaterials 283, 121420

Stealth Effect of Oligo(2-Ethyl-2-Oxazolines) in Graft Copolymers: Minor Changes of Backbone End Group Determine Cell-Type Specificity in the Liver.

Muljajew I*, Huschke S*, Ramoji A, Cseresnyés Z, Hoeppener S, Nischang I, Foo W, Popp J, Figge MT, Weber C, Bauer M, Schubert U, Press A

ACS Nano 15(7), 12298-313.

Enhanced segmentation of label-free cells for automated migration and interaction tracking

Belyaev I, Praetorius JP, Medyukhina A, Figge MT

Cytometry Part A

Comparative assessment of immune evasion mechanisms in human whole-blood infection assays by a systems biology approach.

Lehnert T, Prauße MTE, Hünniger K, Praetorius JP, Kurzai O, Figge MT

PLoS One 16(4), e0249372

Dynamic spherical harmonics approach for shape classification of migrating cells.

Medyukhina A*, Blickensdorf M*, Cseresnyés Z, Ruef N, Stein JV, Figge MT

Sci Rep 10(1), 6072.

MISA++: A standardized interface for automated bioimage analysis

Ruman Gerst, Anna Medyukhina, Marc Thilo Figge*

SoftwareX Volume 11

Automated tracking of label-free cells with enhanced recognition of whole tracks

Al-Zaben N*, Medyukhina A*, Dietrich S, Marolda A, Hünniger K, Kurzai O, Figge MT

Sci Rep 9(1), 3317

Predictive virtual infection modeling of fungal immune evasion in human whole blood.

Prauße MTE, Lehnert T, Timme S, Hünniger K, Leonhardt I, Kurzai O, Figge MT

Front Immunol 9, 560.

Dimensionality of motion and binding valency govern receptor-ligand kinetics as revealed by agent-based modeling.

Lehnert T, Figge MT

Front Immunol 8, 1692.

Untangling cell tracks: Quantifying cell migration by time lapse image data analysis.

Svensson CM, Medyukhina A, Belyaev I, Al-Zaben N, Figge MT

Cytometry A 93(3), 357-370

Hessian-based quantitative image analysis of host- pathogen confrontation assays

Cseresnyes Z*, Kraibooj K*, Figge MT

Cytometry A 93(3), 346-356

Automated quantification of early bone alterations and pathological bone turnover in experimental arthritis by in vivo PET/CT imaging

Hoffmann B*, Svensson C-M*, Straßburger M, Gebser B, Irmler IM, Kamradt T, Saluz HP, Figge MT

Sci Rep 7, 2217

Fully automated evaluation of total glomerular number and capillary tuft size in murine nephritic kidneys using lightsheet microscopy.

Klingberg A, Hasenberg A, Ludwig-Portugall I, Medyukhina A, Männ L, Brenzel A, Engel DR, Figge MT, Kurts C, Gunzer M

J Am Soc Nephrol 28(2), 452-459

Segmentation of clusters by template rotation expectation maximization.

Svensson C-M, Bondoc K G, Pohnert G, Figge MT

Comput Vis Image Underst 152, 64-72.